gcrma.engine2: GCRMA background adjust engine(internal function)
In gcrma: Background Adjustment Using Sequence Information

Description Usage Arguments Details Value Author(s) See Also

This function adjust for non-specific binding when each array has its own probe affinity information. It takes an AffyBatch object of probe intensities and an AffyBatch of probe affinity, returns one matrix of non-specific binding corrected PM probe intensities.

gcrma.engine2(object,pmIndex=NULL,mmIndex=NULL,
              NCprobe=NULL,affinity.info,
              type=c("fullmodel","affinities","mm","constant"),
              k=6*fast+0.5*(1-fast),
              stretch=1.15*fast+1*(1-fast),correction=1,GSB.adjust=TRUE,rho=0.7,
              verbose=TRUE,fast=TRUE)

`object`	an `AffyBatch`. Note: this is an internal function. Optical noise should have been corrected for.
`pmIndex`	Index of PM probes.This will be computed within the function if left `NULL`
`mmIndex`	Index of MM probes.This will be computed within the function if left `NULL`
`NCprobe`	Index of negative control probes. When set as `NULL`,the MM probes will be used. These probes are used to estimate parameters of non-specific binding on each array. These will be also used to estimate probe affinity profiles when affinity.info is not provided.
`affinity.info`	`NULL` or an `AffyBatch` containing the affinities in the `exprs` slot. This object can be created using the function `compute.affinities`.
`type`	"fullmodel" for sequence and MM model. "affinities" for sequence information only. "mm" for using MM without sequence information.
`k`	A tuning factor.
`stretch`	.
`correction`	.
`GSB.adjust`	Logical value. If `TRUE`, probe effects in specific binding will be adjusted.
`rho`	correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.7
`verbose`	Logical value. If `TRUE` messages about the progress of the function is printed.
`fast`	Logicalvalue. If `TRUE` a faster add-hoc algorithm is used.